Serial isolation of multiple dna targets from stool

ABSTRACT

Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting multiple DNA targets from human stool samples.

The present application is a divisional of U.S. patent application Ser.No. 13/469,999, filed May 11, 2012, which claims the benefit of U.S.Provisional Patent Application Ser. No. 61/485,386, filed May 12, 2011,each which is incorporated herein by reference in its entirety.

FIELD OF INVENTION

Provided herein is technology relating to isolating nucleic acids. Inparticular, the technology relates to methods and kits for extractingmultiple DNA targets from human stool samples.

BACKGROUND

Isolating specific target nucleic acids from a sample is an importantstep for many medical diagnostic assays. For example, certain mutationsand methylation states of particular genes are correlated, associated,and/or predictive of disease. DNA harboring these genes can be recoveredfrom a sample and tested for the presence of the particular mutationsand methylation states. While assaying an individual gene isinformative, a more sensitive and specific diagnostic assay targetssuites of genes comprising many members. Such an assay also providesadditional information relating to the origin and stage of disease.

In practice, assaying such a multi-gene panel requires isolating andassaying several genetic targets from a sample. For many detectionmethods, detecting rare mutations or methylation events in a single generequires isolating and testing a large quantity of DNA to obtainsufficient copies of the gene to allow detection of the rare event. Thisproblem is compounded when assaying a panel of genes, each of which mustbe present in a large quantity for a robust diagnostic test. Thus, todetect rare mutations and methylation events in multiple genes, theisolated DNA must be highly concentrated and comprise a substantialportion of the detection assay. This requirement imposes many problems,however. For example, preparing such quantities and concentrations ofDNA requires a large sample as input (i.e., having a mass of manygrams), and thus requires a method that can prepare DNA from a largesample. In addition, assay inhibitors are often isolated andconcentrated with the DNA preparation. Consequently, conventional assaysthat require concentrated DNA also often introduce inhibitory amounts ofinhibitors into the assay. Moreover, if all targets of the panel areextracted and assayed simultaneously, the sensitivity of the assay iscompromised because each gene of the panel composes a smaller fractionof the preparation as more targets are isolated. Also, if all members ofthe panel are extracted together and thus present in the same solution,the sensitivity of an assay directed to detecting any single particulartarget is compromised by interference from the non-target DNA molecules.

In addition, if a particular diagnostic target is present in a sample,it will be present in a small amount, thus providing a challenge formethods designed to detect it. For example, analyses of DNA from stoolsamples are complicated by the fact that large amounts of DNA from othersources are present. For example, bacteria compose approximately 60% ofthe dry mass of feces and the remainder is largely the remains of plantand animal matter ingested as food by the subject. As such, the humansubject's cells, and only those that slough off the lining of thedigestive tract, are a very small fraction of the stool. Furthermore, inassays to detect gene modifications indicative of colon cancer, if acancerous tumor is present in the colon, then cells derived from thattumor would compose only a small fraction of the human subject's gutcells that slough off the digestive tract lining. Consequently, cancercells (and the DNAs they contain) make up a minimal amount of the stoolmass.

Conventional methods and kits for isolating DNA from samples typicallyprepare total DNA (i.e., non-specifically) from the sample.Consequently, total DNA isolated from a stool sample comprises DNA fromthe gut-resident bacteria (and any viruses, eukaryotes, and archaeapresent) along with DNA from the subject sampled. Moreover, conventionalmethods and kits are primarily designed to prepare DNA from smallsamples, e.g., samples having masses of less than 1 gram, e.g., 50 to200 milligrams. Consequently, conventional methods are not applicable tohigh-sensitivity and high-specificity multi-gene panel analyses becausethey cannot prepare sufficient amounts of highly concentrated,inhibitor-free DNA from large samples such as a stool sample. Assaysusing DNA prepared with conventional methods will not provide a samplethat can be assayed with the required sensitivity threshold fordetecting rare mutation or methylation events. Using a conventionalmethod or kit to provide the starting quantities needed to attain suchsensitivity requires multiple DNA extractions (e.g., the use of multiplekits) from multiple samples in addition to extra purification steps toremove inhibitors. Therefore, what is needed is a method of preparingconcentrated, inhibitor-free DNA from a sample for each member of a genepanel for use in diagnostic assays.

SUMMARY

Provided herein is technology relating to isolating nucleic acids. Inparticular, the technology relates to methods and kits for extractingmultiple DNA targets from human stool samples. The DNA solutionsproduced are highly concentrated, i.e., have a large amount of DNA in asmall volume, and contain minimal amounts of substances that inhibitdownstream assays used to test the DNA. Accordingly, the technologyprovided herein finds use in assays that test multi-gene panels,particularly those that detect rare genetic events.

For example, provided herein are methods for isolating a nucleic acidfrom a stool sample comprising contacting a stool sample with atarget-specific capture reagent; binding a target nucleic acid, whenpresent, to the target-specific capture reagent to form a complex;isolating the complex comprising the target-specific capture reagent andthe target nucleic acid, when present, from the stool sample; elutingthe target nucleic acid, when present, from the complex to produce atarget nucleic acid solution comprising the target nucleic acid, whenpresent; and repeating the method using a different target-specificcapture reagent. The methods are appropriate for large samples, e.g.,having a mass of at least 4 grams. Moreover, each eluted target nucleicacid is sufficiently purified, sufficiently concentrated, andsufficiently free of inhibitors such that each eluted target nucleicacid, when present, is detected by a quantitative PCR when the targetnucleic acid solution composes up to approximately one-third of a volumeof the quantitative PCR.

In some embodiments of the methods provided, the target nucleic acid isa human target nucleic acid. In additional embodiments, the targetnucleic acid is a DNA. While not limited in the means by which thenucleic acid is isolated from the stool sample, in some embodiments thetarget-specific capture reagent is a sequence-specific nucleic acidcapture reagent. In some embodiments, the sequence-specific nucleic acidcapture reagent is an oligonucleotide and in some embodiments theoligonucleotide is covalently attached to a magnetic or paramagneticparticle. Some embodiments provide that a magnet is used for theisolating step and some embodiments provide for the simultaneousisolation of more than one target using multiple target-specific capturereagents in a single isolation step.

The methods provided are applicable to many types of assays. Forexample, in some embodiments, the nucleic acid is an RNA and thequantitative PCR is a quantitative RT-PCR. As another example, in someembodiments the target nucleic acid is correlated with a disease stateselected from the set consisting of colon cancer and adenoma.

Stool samples can be taken and prepared in many ways. For example, insome embodiments the stool sample comprises a stool supernatant preparedfrom a stool homogenate. In some embodiments the stool sample comprisesa stool supernatant further treated with polyvinylpolypyrrolidone andguanidine thiocyanate. In some embodiments, the methods compriseexposing the stool sample to a condition that denatures nucleic acidsbefore the contacting step. For example, some embodiments provide thatthe condition that denatures nucleic acids comprises heating at 90° C.for 10 minutes. Some embodiments further provide that the binding stepcomprises incubating at ambient temperature for 1 hour.

Provided herein are methods for the serial extraction of target nucleicacids from a stool sample. Accordingly, in embodiments of the methodsthe repeating step is performed n times to produce n+1 target nucleicacid solutions, each comprising, when present, a different targetnucleic acid. For example, in some embodiments, n is at least 3.

Also provided are methods for isolating a target human DNA from a humanstool sample comprising obtaining a stool sample from a human subject;homogenizing the stool sample in an homogenization buffer to produce anhomogenized stool sample; preparing a stool supernatant from thehomogenized stool sample; treating the stool supernatant withpolyvinylpolypyrrolidone to produce a clarified stool supernatant;adding guanidine thiocyanate a volume of clarified stool supernatant toproduce a solution comprising guanidine thiocyanate; heating thesolution; adding to the solution a target-specific capture reagentcomprising an oligonucleotide covalently attached to a paramagnetic ormagnetic particle, wherein the oligonucleotide is complementary to thetarget human DNA; incubating the solution at ambient temperature toproduce a complex comprising the target-specific capture reagent and thetarget human DNA, if present; exposing the solution to a magnetic fieldto isolate the complex from the solution; retaining the solutionproduced in the preceding step; eluting the target human DNA, ifpresent, from the complex to produce a target nucleic acid solutioncomprising the target nucleic acid, when present; and repeating theheating, adding, incubating, exposing, retaining, and eluting steps ofthe method using a different target-specific capture reagent in theadding step and the solution retained in the retaining step, whereineach eluted target nucleic acid is sufficiently purified, sufficientlyconcentrated, and sufficiently free of inhibitors such that each elutedtarget human DNA, when present, is detected by a quantitative PCR whenthe target nucleic acid solution composes up to approximately one-thirdof a volume of the quantitative PCR. In some embodiments multipletarget-specific capture reagents are added in the adding step.

In some embodiments the stool sample is at least 4 grams. In someembodiments the clarified stool supernatant comprises 2.0-3.0 Mguanidine thiocyanate and in some embodiments the guanidine thiocyanateconcentration is 2.4 M. In some embodiments the guanidine thiocyanate isadded to 10 milliliters of clarified stool supernatant and in someembodiments the solution is heated to 90° C. for 10 minutes. In someembodiments, the target human DNA is from a gene associated with adisease state selected from the set consisting of colon cancer andadenoma. In some embodiments of the methods provided, the repeating stepis performed n times to produce n+1 target nucleic acid solutions, eachcomprising, when present, a different target nucleic acid. For example,in some embodiments, n is at least 3.

Also provided herein are kits for isolating a target human DNA from ahuman stool sample comprising a volume of stool homogenization solutionsuitable for processing a human stool sample having a mass of at least 4grams; a target-specific capture reagent comprising an oligonucleotidecovalently attached to a paramagnetic or magnetic particle, wherein theoligonucleotide is complementary to the target human DNA; and aninstruction for use, wherein the kit produces a solution comprising thetarget human DNA, when present, that is sufficiently purified,sufficiently concentrated, and sufficiently free of inhibitors such thatthe target human DNA, when present, is detected by a quantitative PCRwhen the solution composes up to approximately one-third of a volume ofthe quantitative PCR. In some embodiments of the kits, the kits furthercomprise a magnet. In some embodiments, the kits further comprisepolyvinylpolypyrrolidone and in some embodiments the kits furthercomprise guanidine thiocyanate. In some embodiments, the kits furthercomprise an elution or wash solution.

In addition, provided herein are uses of a target-specific capturereagent comprising an oligonucleotide attached to a paramagnetic ormagnetic particle; polyvinylpolypyrrolidone; guanidine thiocyanate; anda magnet for the manufacture of a kit for isolating a target human DNAfrom a human stool sample having a mass of at least 4 grams, wherein thekit produces a solution comprising the target human DNA, when present,that is sufficiently purified, sufficiently concentrated, andsufficiently free of inhibitors such that the target human DNA, whenpresent, is detected by a quantitative PCR when the solution composes upto approximately one-third of a volume of the quantitative PCR.

Additional embodiments will be apparent to persons skilled in therelevant art based on the teachings contained herein.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the presenttechnology will become better understood with regard to the followingdrawings:

FIG. 1 is a flowchart of the sequential extraction process.

FIG. 2A is a plot showing the results of a quantitative PCR in which asingle extraction from a stool sample recovers most of the target DNA.FIG. 2B shows the concentrations of Gene A and Gene V in nucleic acidsolutions from a first extraction and a second extraction.

FIGS. 3A-3D show plots showing the results of quantitative PCRs in whichthe recoveries of four target DNAs are similar regardless of the orderin which the four target DNAs are extracted from a stool sample.

DETAILED DESCRIPTION

Provided herein is technology relating to isolating nucleic acids. Inparticular, the technology relates to methods and kits for extractingmultiple DNA targets from human stool samples.

Accordingly, provided herein are methods for producing DNA samples fromlarge samples that comprise inhibitors and in which the target DNA is inlow abundance. In particular, the methods are directed to producingconcentrated and highly purified DNA samples having a small volume(e.g., less than 100, and in some cases less than 60 microliters) andthat are substantially and/or effectively free of substances thatinhibit assays used to test the DNA samples (e.g., PCR, INVADER assay,etc.). Such DNA samples find use in diagnostic assays that qualitativelydetect the presence of, or quantitatively measure the activity,expression, or amount of, a gene, a gene variant (e.g., an allele), or agene modification (e.g., methylation) present in a sample taken from apatient. For example, some cancers are correlated with the presence ofparticular mutant alleles or particular methylation states, and thusdetecting and/or quantifying such mutant alleles or methylation stateshas predictive value for the diagnosis and treatment of cancer.

Many valuable genetic markers are present in extremely low amounts insamples and many of the events that produce such markers are rare.Consequently, even sensitive detection methods such as PCR require alarge amount of DNA to provide enough of a low-abundance target to meetor supersede the detection threshold of the assay. Moreover, thepresence of even low amounts of inhibitory substances can compromise theaccuracy and precision of these assays directed to detecting such lowamounts of a target. Accordingly, provided herein are methods providingthe requisite management of volume and concentration to produce such DNAsamples.

DEFINITIONS

To facilitate an understanding of the present technology, a number ofterms and phrases are defined below. Additional definitions are setforth throughout the detailed description.

As used herein, “a” or “an” or “the” can mean one or more than one. Forexample, “a” widget can mean one widget or a plurality of widgets.

As used herein, “a capture reagent” refers to any agent that is capableof binding to an analyte (e.g., a target). Preferably, “a capturereagent” refers to any agent that is capable of specifically binding toan analyte, e.g., having a higher binding affinity and/or specificity tothe analyte than to any other moiety. Any moiety, such as a cell, acellular organelle, an inorganic molecule, an organic molecule and amixture or complex thereof can be used as a capture reagent if it hasthe requisite binding affinity and/or specificity to the analyte. Thecapture reagents can be peptides, proteins, e.g., antibodies orreceptors, oligonucleotides, nucleic acids, vitamins, oligosaccharides,carbohydrates, lipids, small molecules, or a complex thereof. Capturereagents that comprise nucleic acids, e.g., oligonucleotides, maycapture a nucleic acid target by sequence-specific hybridization (e.g.,through the formation of conventional Watson-Crick basepairs), orthrough other binding interactions. When a capture oligonucleotidehybridizes to a target nucleic acid, hybridization may involve a portionof the oligonucleotide, or the complete oligonucleotide sequence, andthe oligonucleotide may bind to a portion of or to the complete targetnucleic acid sequence.

As used herein, the terms “subject” and “patient” refer to any animal,such as a dog, cat, bird, livestock, and particularly a mammal,preferably a human. In some instances, the subject is also a “user” (andthus the user is also the subject or patient).

As used herein, the term “sample” and “specimen” are usedinterchangeably, and in the broadest senses. In one sense, sample ismeant to include a specimen or culture obtained from any source, as wellas biological and environmental samples. Biological samples may beobtained from animals (including humans) and encompass fluids, solids,tissues, and gases. Biological samples include blood products, such asplasma, serum, stool, urine, and the like. Environmental samples includeenvironmental material such as surface matter, soil, mud, sludge,biofilms, water, crystals, and industrial samples. Such examples are nothowever to be construed as limiting the sample types applicable to thepresent invention.

The term “target,” when used in reference to a nucleic acid capture,detection, or analysis method, generally refers to a nucleic acid havinga feature, e.g., a particular sequence of nucleotides to be detected oranalyzed, e.g., in a sample suspected of containing the target nucleicacid. In some embodiments, a target is a nucleic acid having aparticular sequence for which it is desirable to determine a methylationstatus. When used in reference to the polymerase chain reaction,“target” generally refers to the region of nucleic acid bounded by theprimers used for polymerase chain reaction. Thus, the “target” is soughtto be sorted out from other nucleic acid sequences that may be presentin a sample. A “segment” is defined as a region of nucleic acid withinthe target sequence. The term “sample template” refers to nucleic acidoriginating from a sample that is analyzed for the presence of a target.

As used herein, the term “locus” refers to a particular position, e.g.,of a mutation, polymorphism, or a C residue in a CpG dinucleotide,within a defined region or segment of nucleic acid, such as a gene orany other characterized sequence on a chromosome or RNA molecule. Alocus is not limited to any particular size or length, and may refer toa portion of a chromosome, a gene, functional genetic element, or asingle nucleotide or basepair. As used herein in reference to CpG sitesthat may be methylated, a locus refers to the C residue in the CpGdinucleotide.

As used herein, an “inhibitor” means any compound, substance, orcomposition, or combination thereof, that acts to decrease the activity,precision, or accuracy of an assay, either directly or indirectly, withrespect to the activity, precision, or accuracy of the assay when theinhibitor is absent. An inhibitor can be a molecule, an atom, or acombination of molecules or atoms without limitation.

As used herein, the process of passing a mixture through a filter iscalled “filtration”. The liquid produced after filtering a suspension ofa solid in a liquid is called “filtrate”, while the solid remaining inthe filter is called “retentate”, “residue”, or “filtrand”.

As used herein, a “collection liquid” is a liquid in which to place asample to preserve, stabilize, and otherwise maintain its integrity as arepresentative sample of the specimen from which the sample was taken.While not limited in the types of compositions that find use ascollection liquids, examples of collection liquids are aqueous buffersoptionally comprising a preservative and organic solvents, such asacetonitrile.

As used herein, “PVP” refers to polyvinylpyrrolidone, which is awater-soluble polymer made from the monomer N-vinylpyrrolidone. The termPVP is used herein to refer to PVP in various states of cross-linkedpolymerization, including preparations of PVP that may also be known inthe art as polyvinylpolypyrrolidone (PVPP).

As used herein, “insoluble” refers to the property that a substance doesnot substantially dissolve in water and is essentially immiscibletherewith. Upon separation of an aqueous phase from a non-aqueous phase,an insoluble substance does not partition into or partition with theaqueous phase.

As used herein, a “magnet” is a material or object that produces amagnetic field. A magnet may be a permanent magnet or an electromagnet.As used herein, a magnetic particle or bead is responsive to a magneticfield and may be magnetic or paramagnetic.

The term “amplifying” or “amplification” in the context of nucleic acidsrefers to the production of multiple copies of a polynucleotide, or aportion of the polynucleotide, typically starting from a small amount ofthe polynucleotide (e.g., a single polynucleotide molecule), where theamplification products or amplicons are generally detectable.Amplification of polynucleotides encompasses a variety of chemical andenzymatic processes. The generation of multiple DNA copies from one or afew copies of a target or template DNA molecule during a polymerasechain reaction (PCR) or a ligase chain reaction (LCR; see, e.g., U.S.Pat. No. 5,494,810; herein incorporated by reference in its entirety)are forms of amplification. Additional types of amplification include,but are not limited to, allele-specific PCR (see, e.g., U.S. Pat. No.5,639,611; herein incorporated by reference in its entirety), assemblyPCR (see, e.g., U.S. Pat. No. 5,965,408; herein incorporated byreference in its entirety), helicase-dependent amplification (see, e.g.,U.S. Pat. No. 7,662,594; herein incorporated by reference in itsentirety), hot-start PCR (see, e.g., U.S. Pat. Nos. 5,773,258 and5,338,671; each herein incorporated by reference in their entireties),intersequence-specfic PCR, inverse PCR (see, e.g., Triglia, et al et al.(1988) Nucleic Acids Res., 16:8186; herein incorporated by reference inits entirety), ligation-mediated PCR (see, e.g., Guilfoyle, R. et al etal., Nucleic Acids Research, 25:1854-1858 (1997); U.S. Pat. No.5,508,169; each of which are herein incorporated by reference in theirentireties), methylation-specific PCR (see, e.g., Herman, et al., (1996)PNAS 93(13) 9821-9826; herein incorporated by reference in itsentirety), miniprimer PCR, multiplex ligation-dependent probeamplification (see, e.g., Schouten, et al., (2002) Nucleic AcidsResearch 30(12): e57; herein incorporated by reference in its entirety),multiplex PCR (see, e.g., Chamberlain, et al., (1988) Nucleic AcidsResearch 16(23) 11141-11156; Ballabio, et al., (1990) Human Genetics84(6) 571-573; Hayden, et al., (2008) BMC Genetics 9:80; each of whichare herein incorporated by reference in their entireties), nested PCR,overlap-extension PCR (see, e.g., Higuchi, et al., (1988) Nucleic AcidsResearch 16(15) 7351-7367; herein incorporated by reference in itsentirety), real time PCR (see, e.g., Higuchi, et al., (1992)Biotechnology 10:413-417; Higuchi, et al., (1993) Biotechnology11:1026-1030; each of which are herein incorporated by reference intheir entireties), reverse transcription PCR (see, e.g., Bustin, S. A.(2000) J. Molecular Endocrinology 25:169-193; herein incorporated byreference in its entirety), solid phase PCR, thermal asymmetricinterlaced PCR, and Touchdown PCR (see, e.g., Don, et al., Nucleic AcidsResearch (1991) 19(14) 4008; Roux, K. (1994) Biotechniques 16(5)812-814; Hecker, et al., (1996) Biotechniques 20(3) 478-485; each ofwhich are herein incorporated by reference in their entireties).Polynucleotide amplification also can be accomplished using digital PCR(see, e.g., Kalinina, et al., Nucleic Acids Research. 25; 1999-2004,(1997); Vogelstein and Kinzler, Proc Natl Acad Sci USA. 96; 9236-41,(1999); International Patent Publication No. WO05023091A2; US PatentApplication Publication No. 20070202525; each of which are incorporatedherein by reference in their entireties).

The term “polymerase chain reaction” (“PCR”) refers to the method of K.B. Mullis U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,965,188, thatdescribe a method for increasing the concentration of a segment of atarget sequence in a mixture of genomic or other DNA or RNA, withoutcloning or purification. This process for amplifying the target sequenceconsists of introducing a large excess of two oligonucleotide primers tothe DNA mixture containing the desired target sequence, followed by aprecise sequence of thermal cycling in the presence of a DNA polymerase.The two primers are complementary to their respective strands of thedouble stranded target sequence. To effect amplification, the mixture isdenatured and the primers then annealed to their complementary sequenceswithin the target molecule. Following annealing, the primers areextended with a polymerase so as to form a new pair of complementarystrands. The steps of denaturation, primer annealing, and polymeraseextension can be repeated many times (i.e., denaturation, annealing andextension constitute one “cycle”; there can be numerous “cycles”) toobtain a high concentration of an amplified segment of the desiredtarget sequence. The length of the amplified segment of the desiredtarget sequence is determined by the relative positions of the primerswith respect to each other, and therefore, this length is a controllableparameter. By virtue of the repeating aspect of the process, the methodis referred to as the “polymerase chain reaction” (“PCR”). Because thedesired amplified segments of the target sequence become the predominantsequences (in terms of concentration) in the mixture, they are said tobe “PCR amplified” and are “PCR products” or “amplicons.” Those of skillin the art will understand the term “PCR” encompasses many variants ofthe originally described method using, e.g., real time PCR, nested PCR,reverse transcription PCR (RT-PCR), single primer and arbitrarily primedPCR, etc.

As used herein, the term “nucleic acid detection assay” refers to anymethod of determining the nucleotide composition of a nucleic acid ofinterest. Nucleic acid detection assay include but are not limited to,DNA sequencing methods, probe hybridization methods, structure specificcleavage assays (e.g., the INVADER assay, (Hologic, Inc.) and aredescribed, e.g., in U.S. Pat. Nos. 5,846,717, 5,985,557, 5,994,069,6,001,567, 6,090,543, and 6,872,816; Lyamichev et al., Nat. Biotech.,17:292 (1999), Hall et al., PNAS, USA, 97:8272 (2000), and US2009/0253142, each of which is herein incorporated by reference in itsentirety for all purposes); enzyme mismatch cleavage methods (e.g.,Variagenics, U.S. Pat. Nos. 6,110,684, 5,958,692, 5,851,770, hereinincorporated by reference in their entireties); polymerase chainreaction (PCR), described above; branched hybridization methods (e.g.,Chiron, U.S. Pat. Nos. 5,849,481, 5,710,264, 5,124,246, and 5,624,802,herein incorporated by reference in their entireties); rolling circlereplication (e.g., U.S. Pat. Nos. 6,210,884, 6,183,960 and 6,235,502,herein incorporated by reference in their entireties); NASBA (e.g., U.S.Pat. No. 5,409,818, herein incorporated by reference in its entirety);molecular beacon technology (e.g., U.S. Pat. No. 6,150,097, hereinincorporated by reference in its entirety); E-sensor technology(Motorola, U.S. Pat. Nos. 6,248,229, 6,221,583, 6,013,170, and6,063,573, herein incorporated by reference in their entireties);cycling probe technology (e.g., U.S. Pat. Nos. 5,403,711, 5,011,769, and5,660,988, herein incorporated by reference in their entireties); DadeBehring signal amplification methods (e.g., U.S. Pat. Nos. 6,121,001,6,110,677, 5,914,230, 5,882,867, and 5,792,614, herein incorporated byreference in their entireties); ligase chain reaction (e.g., BaranayProc. Natl. Acad. Sci USA 88, 189-93 (1991)); and sandwich hybridizationmethods (e.g., U.S. Pat. No. 5,288,609, herein incorporated by referencein its entirety).

In some embodiments, target nucleic acid is amplified (e.g., by PCR) andamplified nucleic acid is detected simultaneously using an invasivecleavage assay. Assays configured for performing a detection assay(e.g., invasive cleavage assay) in combination with an amplificationassay are described in US Patent Publication US 20090253142 A1(application Ser. No. 12/404,240), incorporated herein by reference inits entirety for all purposes. Additional amplification plus invasivecleavage detection configurations, termed the QuARTS method, aredescribed in U.S. patent application Ser. Nos. 12/946,737; 12/946,745;and 12/946,752, incorporated herein by reference in their entireties forall purposes.

The term “invasive cleavage structure” as used herein refers to acleavage structure comprising i) a target nucleic acid, ii) an upstreamnucleic acid (e.g., an INVADER oligonucleotide), and iii) a downstreamnucleic acid (e.g., a probe), where the upstream and downstream nucleicacids anneal to contiguous regions of the target nucleic acid, and wherean overlap forms between the a 3′ portion of the upstream nucleic acidand duplex formed between the downstream nucleic acid and the targetnucleic acid. An overlap occurs where one or more bases from theupstream and downstream nucleic acids occupy the same position withrespect to a target nucleic acid base, whether or not the overlappingbase(s) of the upstream nucleic acid are complementary with the targetnucleic acid, and whether or not those bases are natural bases ornon-natural bases. In some embodiments, the 3′ portion of the upstreamnucleic acid that overlaps with the downstream duplex is a non-basechemical moiety such as an aromatic ring structure, e.g., as disclosed,for example, in U.S. Pat. No. 6,090,543, incorporated herein byreference in its entirety. In some embodiments, one or more of thenucleic acids may be attached to each other, e.g., through a covalentlinkage such as nucleic acid stem-loop, or through a non-nucleic acidchemical linkage (e.g., a multi-carbon chain).

As used herein, the terms “complementary” or “complementarity” used inreference to polynucleotides (i.e., a sequence of nucleotides) refers topolynucleotides related by the base-pairing rules. For example, thesequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.”Complementarity may be “partial,” in which only some of the nucleicacids' bases are matched according to the base pairing rules. Or, theremay be “complete” or “total” complementarity between the nucleic acids.The degree of complementarity between nucleic acid strands hassignificant effects on the efficiency and strength of hybridizationbetween nucleic acid strands. This is of particular importance inamplification reactions, as well as detection methods that depend uponbinding between nucleic acids.

As used herein, the term “primer” refers to an oligonucleotide, whetheroccurring naturally, as in a purified restriction digest, or producedsynthetically, that is capable of acting as a point of initiation ofsynthesis when placed under conditions in which synthesis of a primerextension product that is complementary to a nucleic acid strand isinduced (e.g., in the presence of nucleotides and an inducing agent suchas a biocatalyst (e.g., a DNA polymerase or the like). The primer istypically single stranded for maximum efficiency in amplification, butmay alternatively be partially or completely double stranded. Theportion of the primer that hybridizes to a template nucleic acid issufficiently long to prime the synthesis of extension products in thepresence of the inducing agent. The exact lengths of the primers willdepend on many factors, including temperature, source of primer and theuse of the method. Primers may comprise labels, tags, capture moieties,etc.

As used herein, the term “nucleic acid molecule” refers to any nucleicacid containing molecule, including but not limited to, DNA or RNA. Theterm encompasses sequences that include any of the known base analogs ofDNA and RNA including, but not limited to, 4 acetylcytosine,8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine,5-(carboxyhydroxyl-methyl)uracil, 5-fluorouracil, 5-bromouracil,5-carboxymethylaminomethyl-2-thiouracil,5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine,N6-isopentenyladenine, 1-methyladenine, 1-methylpseudo-uracil,1-methylguanine, 1-methylinosine, 2,2-dimethyl-guanine, 2-methyladenine,2-methylguanine, 3-methyl-cytosine, 5-methylcytosine, N6-methyladenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxy-amino-methyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarbonylmethyluracil, 5-methoxyuracil,2-methylthio-N-isopentenyladenine, uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine,2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,5-methyluracil, N-uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and2,6-diaminopurine.

As used herein, the term “nucleobase” is synonymous with other terms inuse in the art including “nucleotide,” “deoxynucleotide,” “nucleotideresidue,” “deoxynucleotide residue,” “nucleotide triphosphate (NTP),” ordeoxynucleotide triphosphate (dNTP).

An “oligonucleotide” refers to a nucleic acid that includes at least twonucleic acid monomer units (e.g., nucleotides), typically more thanthree monomer units, and more typically greater than ten monomer units.The exact size of an oligonucleotide generally depends on variousfactors, including the ultimate function or use of the oligonucleotide.To further illustrate, oligonucleotides are typically less than 200residues long (e.g., between 15 and 100), however, as used herein, theterm is also intended to encompass longer polynucleotide chains.Oligonucleotides are often referred to by their length. For example a 24residue oligonucleotide is referred to as a “24-mer”. Typically, thenucleoside monomers are linked by phosphodiester bonds or analogsthereof, including phosphorothioate, phosphorodithioate,phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,phosphoranilidate, phosphoramidate, and the like, including associatedcounterions, e.g., H⁺, NH₄ ⁺, Na⁺, and the like, if such counterions arepresent. Further, oligonucleotides are typically single-stranded.Oligonucleotides are optionally prepared by any suitable method,including, but not limited to, isolation of an existing or naturalsequence, DNA replication or amplification, reverse transcription,cloning and restriction digestion of appropriate sequences, or directchemical synthesis by a method such as the phosphotriester method ofNarang et al. (1979) Meth Enzymol. 68: 90-99; the phosphodiester methodof Brown et al. (1979) Meth Enzymol. 68: 109-151; thediethylphosphoramidite method of Beaucage et al. (1981) TetrahedronLett. 22: 1859-1862; the triester method of Matteucci et al. (1981) J AmChem Soc. 103:3185-3191; automated synthesis methods; or the solidsupport method of U.S. Pat. No. 4,458,066, entitled “PROCESS FORPREPARING POLYNUCLEOTIDES,” issued Jul. 3, 1984 to Caruthers et al., orother methods known to those skilled in the art. All of these referencesare incorporated by reference.

A “sequence” of a biopolymer refers to the order and identity of monomerunits (e.g., nucleotides, amino acids, etc.) in the biopolymer. Thesequence (e.g., base sequence) of a nucleic acid is typically read inthe 5′ to 3′ direction.

The term “wild-type” refers to a gene or gene product that has thecharacteristics of that gene or gene product when isolated from anaturally occurring source. A wild-type gene is that which is mostfrequently observed in a population and is thus arbitrarily designed the“normal” or “wild-type” form of the gene. In contrast, the terms“modified,” “mutant,” and “variant” refer to a gene or gene product thatdisplays modifications in sequence and or functional properties (i.e.,altered characteristics) when compared to the wild-type gene or geneproduct. It is noted that naturally occurring mutants can be isolated;these are identified by the fact that they have altered characteristicswhen compared to the wild-type gene or gene product.

As used herein, the term “gene” refers to a nucleic acid (e.g., DNA)sequence that comprises coding sequences necessary for the production ofa polypeptide, precursor, or RNA (e.g., rRNA, tRNA). The polypeptide canbe encoded by a full length coding sequence or by any portion of thecoding sequence so long as the desired activity or functional properties(e.g., enzymatic activity, ligand binding, signal transduction,immunogenicity, etc.) of the full-length or fragment polypeptide areretained. The term also encompasses the coding region of a structuralgene and the sequences located adjacent to the coding region on both the5′ and 3′ ends for a distance of about 1 kb or more on either end suchthat the gene corresponds to the length of the full-length mRNA.Sequences located 5′ of the coding region and present on the mRNA arereferred to as 5′ non-translated sequences. Sequences located 3′ ordownstream of the coding region and present on the mRNA are referred toas 3′ non-translated sequences. The term “gene” encompasses both cDNAand genomic forms of a gene. A genomic form or clone of a gene containsthe coding region interrupted with non-coding sequences termed “introns”or “intervening regions” or “intervening sequences.”Introns are segmentsof a gene that are transcribed into nuclear RNA (e.g., hnRNA); intronsmay contain regulatory elements (e.g., enhancers). Introns are removedor “spliced out” from the nuclear or primary transcript; intronstherefore are absent in the messenger RNA (mRNA) transcript. The mRNAfunctions during translation to specify the sequence or order of aminoacids in a nascent polypeptide.

In addition to containing introns, genomic forms of a gene may alsoinclude sequences located on both the 5′ and 3′ end of the sequencesthat are present on the RNA transcript. These sequences are referred toas “flanking” sequences or regions (these flanking sequences are located5′ or 3′ to the non-translated sequences present on the mRNAtranscript). The 5′ flanking region may contain regulatory sequencessuch as promoters and enhancers that control or influence thetranscription of the gene. The 3′ flanking region may contain sequencesthat direct the termination of transcription, post-transcriptionalcleavage and polyadenylation.

As used herein, the term “kit” refers to any delivery system fordelivering materials. In the context of nucleic acid purificationsystems and reaction assays, such delivery systems include systems thatallow for the storage, transport, or delivery of reagents and devices(e.g., inhibitor adsorbants, particles, denaturants, oligonucleotides,spin filters etc. in the appropriate containers) and/or supportingmaterials (e.g., buffers, written instructions for performing aprocedure, etc.) from one location to another. For example, kits includeone or more enclosures (e.g., boxes) containing the relevant reactionreagents and/or supporting materials. As used herein, the term“fragmented kit” refers to a delivery system comprising two or moreseparate containers that each contains a subportion of the total kitcomponents. The containers may be delivered to the intended recipienttogether or separately. For example, a first container may contain anmaterials for sample collection and a buffer, while a second containercontains capture oligonucleotides and denaturant. The term “fragmentedkit” is intended to encompass kits containing Analyte specific reagents(ASR's) regulated under section 520(e) of the Federal Food, Drug, andCosmetic Act, but are not limited thereto. Indeed, any delivery systemcomprising two or more separate containers that each contains asubportion of the total kit components are included in the term“fragmented kit.” In contrast, a “combined kit” refers to a deliverysystem containing all of the components of a reaction assay in a singlecontainer (e.g., in a single box housing each of the desiredcomponents). The term “kit” includes both fragmented and combined kits.

The term “system” as used herein refers to a collection of articles foruse for a particular purpose. In some embodiments, the articles compriseinstructions for use, as information supplied on e.g., an article, onpaper, or on recordable media (e.g., diskette, CD, flash drive, etc.).In some embodiments, instructions direct a user to an online location,e.g., a website.

As used herein, the term “information” refers to any collection of factsor data. In reference to information stored or processed using acomputer system(s), including but not limited to internets, the termrefers to any data stored in any format (e.g., analog, digital, optical,etc.). As used herein, the term “information related to a subject”refers to facts or data pertaining to a subject (e.g., a human, plant,or animal). The term “genomic information” refers to informationpertaining to a genome including, but not limited to, nucleic acidsequences, genes, percentage methylation, allele frequencies, RNAexpression levels, protein expression, phenotypes correlating togenotypes, etc. “Allele frequency information” refers to facts or datapertaining to allele frequencies, including, but not limited to, alleleidentities, statistical correlations between the presence of an alleleand a characteristic of a subject (e.g., a human subject), the presenceor absence of an allele in an individual or population, the percentagelikelihood of an allele being present in an individual having one ormore particular characteristics, etc.

Embodiments of the Technology

Although the disclosure herein refers to certain illustratedembodiments, it is to be understood that these embodiments are presentedby way of example and not by way of limitation.

Provided herein are methods for isolating DNA, for example from a stoolsample. As summarized in FIG. 1, the process comprises homogenizing asample (e.g., a stool sample) in a suitable buffer and preparing asupernatant from the homogenate. The supernatant is treated with acomposition (e.g., a cross-linked polyvinylpyrrolidone (PVP) such aspolyvinylpolypyrrolidone (PVPP); see, e.g., U.S. Patent Appln. Ser. No.61/485,338 to Bruinsma, which is incorporated herein by reference in itsentirety) to remove inhibitors and produce a clarified supernatant. DNAin the clarified supernatant is denatured, e.g., by adding guanidinethiocyanate and/or by heating the sample. Then, a target capturereagent, e.g., a magnetic bead to which is linked an oligonucleotidecomplementary to the target, is added and the solution is incubatedunder conditions (e.g., ambient temperature for an hour) that promotethe association (e.g., by hybridization) of the target with the capturereagent to produce a target:capture reagent complex. After isolating andremoving the target:capture reagent complex (e.g., by application of amagnetic field), the resulting solution is heated again to denature theremaining DNA in the clarified supernatant and another target capturereagent can be added to isolate another target. The process can berepeated, to isolate additional targets that are required for the assayor for other purposes. The isolated target:capture reagent complexesfrom each capture and isolation step are washed and the target DNAs areeluted using a small volume of buffer suitable for downstream analysis.

Moreover, multiple targets can be isolated in each round of isolation byadding multiple target capture reagents to the solution. For example,multiple target capture reagents, each comprising an oligonucleotidespecific for a different target can be added to the solution forisolation of multiple targets, then the retained supernatant can be usedagain for additional, repeated isolation of one or more other targets.It is contemplated that the methods encompass multiple experimentaldesigns that vary both in the number of capture steps and in the numberof targets captured in each capture step.

Capture Reagents

In one aspect, the methods provided herein relate to the use of capturereagents. Such reagents are molecules, moieties, substances, orcompositions that preferentially (i.e., specifically and selectively)interact with a particular target sought to be isolated and purified.Any capture reagent having desired binding affinity and/or specificityto the analyte target can be used in the present technology. Forexample, the capture reagent can be a macromolecule such as a peptide, aprotein (e.g., an antibody or receptor), an oligonucleotide, a nucleicacid, (e.g., nucleic acids capable of hybridizing with the targetnucleic acids), vitamins, oligosaccharides, carbohydrates, lipids, orsmall molecules, or a complex thereof. As illustrative and non-limitingexamples, an avidin target capture reagent may be used to isolate andpurify targets comprising a biotin moiety, an antibody may be used toisolate and purify targets comprising the appropriate antigen orepitope, and an oligonucleotide may be used to isolate and purify acomplementary oligonucleotide (e.g., a poly-dT oligonucleotide may beused to isolate and purify targets comprising a poly-A tail).

Any nucleic acids, including single-, double-, and triple-strandednucleic acids, that are capable of binding, or specifically binding, tothe target can be used as the capture reagent in the present device.Examples of such nucleic acids include DNA, such as A-, B- or Z-formDNA, and RNA, such as mRNA, tRNA and rRNA, aptamers, peptide nucleicacids, and other modifications to the sugar, phosphate, or nucleosidebase. Thus, there are many strategies for capturing a target andaccordingly many types of capture reagents are known to those in theart. While not limited in the means by which a target nucleic acid canbe captured, embodiments of the technology provided herein compriseusing an oligonucleotide that is complementary to the target and thatthus captures the target by specifically and selectively hybridizing tothe target nucleic acid.

In addition, target capture reagents comprise a functionality tolocalize, concentrate, aggregate, etc. the capture reagent and thusprovide a way to isolate and purify the target when captured (e.g.,bound, hybridized, etc.) to the capture reagent, i.e., when atarget:capture reagent complex is formed. For example, in someembodiments the portion of the target capture reagent that interactswith the target (e.g., the oligonucleotide) is linked to a solid support(e.g., a bead, surface, resin, column, and the like) that allowsmanipulation by the user on a macroscopic scale. Often, the solidsupport allows the use of a mechanical means to isolate and purify thetarget:capture reagent complex from a heterogeneous solution. Forexample, when linked to a bead, separation is achieved by removing thebead from the heterogeneous solution, e.g., by physical movement. Inembodiments in which the bead is magnetic or paramagnetic, a magneticfield is used to achieve physical separation of the capture reagent (andthus the target) from the heterogeneous solution. Magnetic beads used toisolate targets are described in the art, e.g., as described in EuropeanPatent Application No. 87309308, incorporated herein in its entirety forall purposes.

EXAMPLES Example 1

During the development of embodiments of the technology provided herein,it was demonstrated that the majority of the DNA for a given target isdepleted from a stool supernatant in a single isolation. The isolationwas performed according to the flow chart shown in FIG. 1. After finalelution, the recoveries of the two targets (Gene A and Gene V) fromisolations 1 and 2 were monitored by SYBR Green qPCR assays using 1microliter of eluate in a 25-microliter volume reaction. For bothtargets, isolation 1 yielded good recovery of target, whereas the eluatefrom isolation 2 failed to produce any qPCR signal for either target(FIG. 2).

Example 2

During the development of embodiments of the technology provided herein,it was demonstrated that DNA isolation can be performed repeatedly on asingle sample through a minimum of four cycles of denaturation andhybridization without compromising the integrity of the human DNA in thestool supernatant. In this example, four targets (Genes A, F, V, and W)were captured from the sample and the order of their capture was varied.After elution, the recovery of each target was monitored by SYBR GreenqPCR. In FIG. 3, plots show the amplification curves for each gene whenit was captured first, second, third, and fourth in the sequence ofisolations. The superposition of the amplification curves demonstratesthat recoveries were approximately equal regardless of the order ofisolation. Table 1 quantifies the results from FIG. 3.

TABLE 1 Target Isolation Mean C_(p) Mean Strands/μL Gene A #1 28.92 862#2 28.89 878 #3 28.85 907 #4 28.73 984 Gene F #1 29.32 499 #2 29.36 489#3 29.29 511 #4 29.01 614 Gene V #1 31.29 129 #2 31.01 155 #3 31.18 139#4 30.84 177 Gene W #1 29.17 724 #2 29.11 757 #3 28.99 819 #4 29.16 730

For all four genes, the mean C_(p) (Crossing point—the cycle number atwhich the amplification curve crosses a fixed threshold) and strandnumbers were essentially equal regardless of the order of extraction.

Example 3 Exemplary Procedure for Serial Isolation of a Plurality ofTarget Nucleic Acids As Diagrammed in FIG. 1:

-   -   1. A stool sample is homogenized, e.g., with a buffer, to form a        stool homogenate. The homogenate treated to partition residual        solids from the fluid, e.g., by centrifugation or filtration, to        produce a “stool supernatant.”    -   2. Stool supernatant is treated to remove assay inhibitors        (e.g., with polyvinylpolypyrrolidone, as described in U.S. Pat.        Appl. Ser. No. 61/485,338, which is incorporated herein by        reference in its entirety), producing “clarified supernatant”.    -   3. Ten milliliters of clarified supernatant (representing an        equivalent of approximately 4 grams of stool) is mixed with        guanidine thiocyanate (GTC) to a final concentration of 2.4 M;    -   4. The mixture is then heated in a 90° C. water bath for 10        minutes to denature the DNA (and proteins) present in the stool.    -   5. Paramagnetic particles containing covalently attached        (coupled) oligonucleotides complementary to the target        sequence(s) of interest (“target-specific capture probes”) are        added to the sample. The sample is then incubated (e.g., at        ambient temperature, about 22-25° C.) for one hour to enable        hybridization of the target DNA to the capture probes on the        magnetic particles.    -   6. The mixture of clarified supernatant, GTC, and particles is        exposed to a magnetic field to separate the particles (now        containing target DNA hybridized to the capture probes) from the        stool supernatant/GTC mixture, which is transferred to a new        tube. See, e.g., U.S. patent application Ser. No. 13/089,116,        which is incorporated herein by reference.    -   7. The paramagnetic particles are then washed and the target DNA        eluted, ready for use in detection assays.    -   8. The supernatant/GTC mixture retained in step 6 is returned to        the 90° C. water bath for 10 minutes to repeat denaturation        (step 4). Step 5 is then repeated by adding magnetic particles        containing capture probes complementary to different targets        DNAs, and the hybridization, particle separation and elution        steps are repeated to produce a purified sample of a second DNA        target.

The denaturation/hybridization/separation cycle (steps 4-6) can berepeated at least four or more times to serially extract differenttarget DNAs from the same stool supernatant sample.

All publications and patents mentioned in the above specification areherein incorporated by reference in their entirety for all purposes.Various modifications and variations of the described compositions,methods, and uses of the technology will be apparent to those skilled inthe art without departing from the scope and spirit of the technology asdescribed. Although the technology has been described in connection withspecific exemplary embodiments, it should be understood that theinvention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications of the described modes forcarrying out the invention that are obvious to those skilled in relatedfields (e.g., engineering, mechanics, materials science, or medicaldiagnostics) are intended to be within the scope of the followingclaims.

1.-29. (canceled)
 30. A composition comprising a residual supernatantfrom a human stool homogenate comprising human DNA, said residualsupernatant produced by a method comprising: i) exposing a supernatantfrom a stool homogenate to a plurality of different target-specificcapture reagents, wherein each of said plurality of differenttarget-specific capture reagents forms a complex with a different targethuman DNA, and ii) removing target-specific capture reagent/target humanDNA complexes from said supernatant to produce said residualsupernatant.
 31. The composition of claim 30, wherein each targetspecific capture reagent comprises an oligonucleotide complementary to atarget human DNA.
 32. The composition of claim 31, wherein eacholigonucleotide complementary to a target human DNA is covalentlyattached to a particle.
 33. The composition of claim 32, wherein saidparticle is a magnetic particle.
 34. The composition of claim 30,wherein said stool homogenate comprises at least 4 grams of stool from ahuman subject.
 35. The composition of claim 1, wherein prior to step i),said method comprises heating said supernatant.
 36. The composition ofclaim 35, wherein said heating comprises heating to 90° C.
 37. Thecomposition of claim 30, wherein prior to step i) said method comprisestreating said stool supernatant with polyvinylpyrrolidone.
 38. Thecomposition of claim 37, wherein said polyvinylpyrrolidone ispolyvinylpolypyrrolidone.
 39. The composition of claim 30, wherein saidsupernatant from a stool homogenate comprises guanidine thiocyanate. 40.The composition of claim 39, wherein said guanidine thiocyanate ispresent at a concentration of 2-3 M.
 41. The composition of claim 30,wherein said plurality of different target-specific capture reagentscomprises at least 3 different target-specific capture reagents.
 42. Thecomposition of claim 30, wherein said plurality of differenttarget-specific capture reagents comprises at least 4 differenttarget-specific capture reagents.
 43. The composition of claim 30,wherein one or more of said target human DNAs are from genes associatedwith a disease state selected from the group consisting of colorectalcancer and colorectal adenoma.